ASpli 1.0.0
Estefania Mancini
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ASpli | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf ASpli.buildbin-libdir ASpli.Rcheck && mkdir ASpli.buildbin-libdir ASpli.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ASpli.buildbin-libdir ASpli_1.0.0.tar.gz >ASpli.Rcheck\00install.out 2>&1 && cp ASpli.Rcheck\00install.out ASpli-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ASpli.buildbin-libdir --install="check:ASpli-install.out" --force-multiarch --no-vignettes --timings ASpli_1.0.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/ASpli.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ASpli/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASpli' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'GenomicRanges' 'GenomicFeatures' 'edgeR' 'BiocGenerics' 'IRanges'
'GenomicAlignments' 'DESeq2' 'DEXSeq' 'Gviz' 'S4Vectors'
'AnnotationDbi' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ASpli' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readCounts,ASpliFeatures: no visible binding for global variable
'targets'
Undefined global functions or variables:
targets
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DUreport_DEXSeq 111.02 6.33 117.34
ASpli-package 88.35 7.81 96.21
plotTopTags 74.73 1.79 76.53
acc_AS 72.90 3.26 76.17
AsDiscover-methods 67.74 5.82 73.54
DUreport 66.67 4.56 71.24
acc_counts 66.47 2.39 68.86
readCounts 67.18 1.65 68.82
acc_DU 65.42 1.71 67.13
loadBAM 12.50 0.46 12.96
binGenome 9.61 0.03 9.64
acc_features 9.42 0.04 9.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DUreport_DEXSeq 120.41 5.33 125.74
ASpli-package 88.55 8.30 96.89
acc_AS 81.09 2.49 83.57
AsDiscover-methods 76.42 6.37 82.82
plotTopTags 75.69 2.61 78.30
readCounts 64.64 4.47 69.11
DUreport 64.59 3.70 68.29
acc_counts 64.53 3.63 68.17
acc_DU 64.06 3.29 67.60
acc_features 11.29 0.04 11.33
binGenome 10.54 0.02 10.56
loadBAM 10.05 0.45 10.50
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/ASpli.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ASpli' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'ASpli' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASpli' as ASpli_1.0.0.zip
* DONE (ASpli)